Malaria, caused by protozoan parasites in the genus Plasmodium and transmitted by Anopheles mosquitoes, is a disease of critical importance to global public health. The premise of our proposal is that genomic resources and technology development have the potential to greatly contribute to the renewed malaria elimination effort through enhanced biological and epidemiological understanding. The work described in this study will advance our understanding of parasite/vector interactions, parasite/human interactions, vector evolution, and parasite genomic epidemiology. AIM 1. Develop a major population genomic resource for Neotropical anopheline malaria vectors. We will generate two significantly improved reference genome assemblies for An. darlingi, the most important vector in the New World, and perform resequencing-based population genomic studies of An. darlingi and other neotropical malaria vectors to identify cryptic species boundaries and population structure that could impact traits contributing to vectorial capacity. AIM 2. Profile the comparative population genomics of malaria parasites in low-transmission settings in West Africa and the Neotropics. Malaria parasites in low-transmission settings typically face distinct challenges from parasites in more highly endemic zones, including reduced host immunity, reduced intra-host competition, higher access to treatment, and concomitantly more consistent selection pressure from drugs. We will perform whole genome sequencing of thousands of P. falciparum parasites from low-transmission settings in the Neotropics and West Africa to identify common as well as distinct population genomic signatures of adaptation and transmission dynamics AIM 3. Identify parasite genes that mediate interactions with mosquito vectors by sequencing a unique sample collection from Gabon. Malaria parasites and anopheline vectors are known to adapt to each other, sometimes on very local geographic scales. We will search for parasite loci that mediate this adaptation by sequencing Plasmodium falciparum from infected mosquitoes collected in Gabon, West Africa, a region where at least 15 anopheline species serve as vectors for three human malaria parasite species. AIM 4. Define the transcriptional profile of the human host and Plasmodium parasites in single infected hepatocytes. The key biological difference between P. falciparum and P. vivax is the capacity of the latter species to remain in a metabolically dormant hypnozoite state within the liver for weeks, months, or years, impervious to most drug treatments. We will study how host and parasite genes are regulated within individual infected hepatocyte cells. This work will influence the field through the generation of novel genomic resources and methods, new biological insights, and innovative analytical methods.